Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class II BoLA-DRB3 allele.

Bovine leukocyte antigens (BoLAs) are used extensively as markers for bovine disease and immunological traits. In this study, we estimated BoLA-DRB3 allele frequencies using 888 cattle from 10 groups, including seven cattle breeds and three crossbreeds: 99 Red Angus, 100 Black Angus, 81 Chilean Wagyu, 49 Hereford, 95 Hereford × Angus, 71 Hereford × Jersey, 20 Hereford × Overo Colorado, 113 Holstein, 136 Overo Colorado, and 124 Overo Negro cattle. Forty-six BoLA-DRB3 alleles were identified, and each group had between 12 and 29 different BoLA-DRB3 alleles. Overo Negro had the highest number of alleles (29); this breed is considered in Chile to be an 'Old type' European Holstein Friesian descendant. By contrast, we detected 21 alleles in Holstein cattle, which are considered to be a 'Present type' Holstein Friesian cattle. Chilean cattle groups and four Japanese breeds were compared by neighbor-joining trees and a principal component analysis (PCA). The phylogenetic tree showed that Red Angus and Black Angus cattle were in the same clade, crossbreeds were closely related to their parent breeds, and Holstein cattle from Chile were closely related to Holstein cattle in Japan. Overall, the tree provided a thorough description of breed history. It also showed that the Overo Negro breed was closely related to the Holstein breed, consistent with historical data indicating that Overo Negro is an 'Old type' Holstein Friesian cattle. This allelic information will be important for investigating the relationship between major histocompatibility complex (MHC) and disease.

Canine parentage testing based on microsatellite polymorphisms.

To establish an accurate method for parentage testing in dogs, microsatellite DNA repeat length polymorphisms were examined. We selected twenty microsatellite markers reported previously and examined their application for parentage testing in Beagles and Labrador Retrievers. Heterozygosity (He), Polymorphism Information Content (PIC), the probabilities of Paternity Exclusion (PE) and the combined PE were calculated from allelic frequencies of the markers. All markers amplified by polymerase chain reactions were polymorphic and many markers showed high He and PIC in the both breeds. The final combined PEs in Beagles and Labrador Retrievers were 0.999994 and 0.999920, respectively. The results suggest that the twenty markers can be applied for routine parentage testing in dogs.

Use of microsatellite markers for parentage testing of two litters of beagles born after artifcial insemination with mixed fresh semen.

This study was undertaken to determine if 20 kinds of microsatellite markers, which have already been reported, were useful for the parentage testing of 16 Beagle puppies born after artificial insemination using intentionally mixed semen from six male Beagles. Of the 20 kinds of markers used in this study, 17 kinds (the exceptions were CPH6, FH0020 and FH0419) produced 3 to 5 kinds of alleles, and using these markers, the parentage was finally established for all of the 16 puppies. These 17 kinds of markers showed sufficient amplification in PCR and had no non-specific PCR products or alleles with single-base-alterations, which makes them very useful as markers for identification of individual Beagles and useful for parentage testing.

Chromosome mapping and expression of human tip49 family genes.

TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. At least, TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases. In this study, we investigated the chromosome positions of this family of genes. Human tip49a and tip49b genes were mapped on 3q21 and 19q13.2, respectively. Consistent with the notion that tip49 family genes are essential for cell growth, Northern blot analysis demonstrated that both genes are expressed ubiquitously in human tissues. It is worthy of notice that the testes contained large amounts of the both transcripts. These results are consistent with our previous results from tissue distribution analysis for of TIP49 proteins.

A notable example of an evolutionary conserved gene: studies on a putative DNA helicase TIP49.

TIP49a (just called as simply TIP49 in previous reports [Kanemaki et al., 1997; Makino et al., 1998]) was found in a rat nuclear protein complex that included the TATA-binding protein. TIP49a possesses multiple sequence motifs for ATPase and DNA helicase. Since TIP49a structurally resembles prokaryotic DNA helicase RuvB, TIP49a is resumed to be a putative DNA helicase. We demonstrated TIP49a-related gene(s) in variety organisms from human to archaea. Amino acid identities expressed as aligned scores of human, yeast, and A. fulgidus TIP49a gene counterparts to the rat sequence were 99, 67, and 46, respectively. Strikingly, two homologous regions of mammalian TIP49a and bacterial RuvB exhibited an aligned score of 17-38. We demonstrated that the eukaryotic TIP49a counterparts were immunologically conserved. These lines of evidence show that the TIP49a gene is a notable example of a highly conserved gene among organisms. An extensive homology search revealed another class of TIP49-related gene in the eukaryotes, designated as TIP49b. Moreover, a phylogenetical study suggested that archaeal TIP49 genes belong to the TIP49b ancestor but not to the TIP49a one and that TIP49a evolved from TIP49b in accordance with divergence of archaea and eukarya. The TIP49 gene family is thought to play a fundamental role in a biological activity.

TIP49b, a new RuvB-like DNA helicase, is included in a complex together with another RuvB-like DNA helicase, TIP49a.

We previously reported that TIP49a is a novel mammalian DNA helicase showing structural similarity with the bacterial recombination factor RuvB. In this study, we isolated a new TIP49a-related gene, termed TIP49b, from human and yeast cells. TIP49b also resembled RuvB, thus suggesting that TIP49a and TIP49b are included in a gene family. Like TIP49a, TIP49b was abundantly expressed in the testis and thymus. Enzyme assays revealed that TIP49b was an single-stranded DNA-stimulated ATPase and ATP-dependent DNA helicase. Most of the enzymatic properties of TIP49b were the same as those of TIP49a, whereas the polarity of TIP49b DNA helicase activity (5' to 3') was the opposite to that of TIP49a. TIP49b and TIP49a bound to each other and were included in the same complex of approximately 700 kDa in a cell. We found that TIP49b was an essential gene for the growth of Saccharomyces cerevisiae, as is the TIP49a gene, suggesting that TIP49b does not complement the TIP49a function and vice versa. From these observations, we suggest that TIP49b plays an essential role in the cellular processes involved in DNA metabolism.

A rat RuvB-like protein, TIP49a, is a germ cell-enriched novel DNA helicase.

We have isolated a novel nuclear protein with a molecular mass of 49 kDa (TIP49a) from rat liver. The rat TIP49a showed structural resemblance to several bacterial RuvBs and also displayed Walker A and B motifs. We overproduced the recombinant TIP49a in Escherichia coli and purified it to near homogeneity. Biochemical investigations demonstrated that TIP49a possessed ATPase activity that was stimulated by single-stranded DNA but neither by double-stranded DNA nor by any forms of RNA polymers tested. Moreover, a UV cross-linking assay indicated TIP49a specifically interacted with ATP. Interestingly, we found that DNA duplex was unwound by the recombinant TIP49a in the presence of ATP or dATP. Optimal concentrations of ATP and Mg2+ for the helicase activity were 1-2 mM and 0.25-1 mM, respectively. Displacement of the DNA strand occurred in the 3' to 5' direction with respect to the single-stranded DNA flanking the duplex. Western blot analysis revealed that TIP49a was abundantly expressed in testes and moderately in spleen, thymus, and lung. In mouse seminiferous tubules, the protein was restrictively observed in germ lineages from late pachytene spermatocytes to round spermatids. From these observations, we propose that TIP49a is a novel DNA helicase and may play a role in nuclear processes such as recombination and transcription.

TIP49, homologous to the bacterial DNA helicase RuvB, acts as an autoantigen in human.

TATA-binding protein (TBP), a central component for transcriptional regulation, forms complexes with various transcription regulators. We have isolated a novel human cDNA for a 49-kD TBP-interacting protein (TIP49). The human TIP49 was highly homologous to bacterial RuvB proteins that function as a DNA helicase to promote branch migration of the Holliday junction. Immunofluorescence analysis using anti-TIP49 antibody showed a typical dot-shaped nuclear staining pattern, suggesting that TIP49 is included in a macromolecular structure in the nucleus and may participate in nuclear events such as transcription and recombination. Moreover, glycerol gradient analysis demonstrated that TIP49 is present in a macromolecular complex in nuclear extracts. Interestingly, we detected a high level of autoantibodies against TIP49 in sera of patients with autoimmune diseases such as polymyositis/dermatomyositis and autoimmune hepatitis. This indicates that the autoantibody against this protein is a new marker for particular connective tissue diseases. These findings provide further evidence that the macromolecular structures described above are targeted by an autoimmune mechanism. The anti-TIP49 antibodies can be useful probes for clinical diagnosis and for investigation of intranuclear structure.

SUG1, a component of the 26 S proteasome, is an ATPase stimulated by specific RNAs.

SUG1 is an integral component of the 26 S proteasome. Belonging to a novel putative ATPase family, it shares four conserved motifs characteristic of ATP-dependent DNA/RNA helicases. Recombinant rat SUG1 (rSUG1) produced in Escherichia coli was highly purified and characterized in terms of its biochemical properties. The rSUG1 exhibited a Mg2+-dependent ATPase activity. The Km for ATP and Vmax of rSUG1 were 35 microM and 7 pmol of ATP/min/microg of protein, respectively. Both ATPase activity to release [32P]monophosphate and [32P]ATP-labeling activity were coordinately affected by cold ATP severely, GTP and UTP moderately, and CTP little. Interestingly, the rSUG1 ATPase activity was stimulated by poly(U) and poly(C), but not by poly(A), poly(G), or by any forms of DNAs tested. A UV cross-linking assay also indicated poly(U)- and poly(C)-stimulated labeling of rSUG1 with [alpha-32P]ATP. Moreover, the ATPase activity was facilitated by cellular poly(A)+ RNA, but not by poly(A)- RNA. RNA transcribed in vitro from cDNA encoding a b-Zip protein could stimulate the ATPase activity. This is the first report to demonstrate a specific RNA requirement for ATPase with respect to the proteasomal ATPases. Our present work suggests that SUG1 can specifically interact with protein-coding RNA (mRNA) and play some roles in mRNA metabolism.

Molecular cloning of a rat 49-kDa TBP-interacting protein (TIP49) that is highly homologous to the bacterial RuvB.

TBP as a central component in transcriptional regulation can form complexes with various regulatory factors. Using histidine-tagged TBP for affinity-purification of TBP-bound proteins, we isolated a 49-kD protein termed TBP-interacting protein 49 (TIP49) from rat liver nuclear extracts. We cloned the entire cDNA of TIP49 encoding a novel polypeptide of 456 amino acids, and thereafter established an FM3A cell line that constitutively expressed an epitope-tagged TBP. Immunoprecipitation analysis of the cell extracts indicated that TIP49 and TBP were present in an identical complex. Interestingly, the amino acid sequence of TIP49 exhibited high similarity to those sequences of the RuvB bacterial recombination factors which direct branch migration of the Holliday junction and contain the Walker A and B motifs responsible for ATP binding and ATP hydrolysis. These findings suggest that TIP49 is a putative ATP-dependent DNA helicase.

Structures of the rat proteasomal ATPases: determination of highly conserved structural motifs and rules for their spacing.

We have isolated rat cDNAs for all of the five known proteasomal ATPases. The protein sequences of rat TBP1, TBP7, MSS1, S4, and SUG1 predicted from the open reading frames consist of 439, 418, 433, 440, and 406 amino acid residues, respectively, and exhibit striking similarities to each human counterpart with only several amino acid substitutions. These five rat ATPases are also highly homologous with each other. The N-terminal region in rat TBP1, TBP7, and SUG1 contains a heptad repeat of hydrophobic amino acids reminiscent of a leucine zipper. Also, in the central region of each rat ATPase, we found four conserved motifs, Gx4GKT, DEID, SAT, and H/QRxGRx2R, that are characteristic of a large family of ATP-dependent RNA/DNA helicases. The spacing between individual motifs was strictly conserved in the rat ATPases. These findings suggest a common function of the rat proteasomal ATPases in ATP-dependent RNA/DNA unwinding.

[Correlation between fetal growth and platelet function in normal pregnancy].

Various interpretations have been attempted, but no definitive theory has yet been established as to the etiology of the low-birth-weight infant. We carried out the present study in an attempt to explore the relationship between platelet functions and fetal growth during normal pregnancy. For this purpose, we made a retrospective study of 130 pregnant women aged 23-35 with no clinical abnormalities throughout pregnancy or at delivery. Blood samples were taken at 29-30 weeks of gestation (referred to as the 2nd trimester) and 37-38 weeks of gestation (referred to as the 3rd trimester). The cases studied were divided into two groups: i) those with a birth weight of under 2,500g (n = 32), and ii) those with a birth weight of over 2,500g (n = 98). In these two groups, we studied the platelet functions in maternal blood in the 2nd and 3rd trimesters. The following results were obtained: 1) In the 2nd to 3rd trimester, the platelet count showed no significant variation with the birth weight. 2) In the 2nd to 3rd trimester, the platelet aggregation was found to be moderately depressed in cases with a birth weight of under 2,500g, while it was found to be moderately activated in cases with a birth weight of over 2,500g. 3) In the 2nd to 3rd trimester, platelet factor 4 was significantly lower (p < 0.005) in cases with a birth weight of under 2,500g, while it was moderately higher in cases with a birth weight of over 2,500g.(ABSTRACT TRUNCATED AT 250 WORDS)